I created a batch file to compare a snapshot against a database. A project was created using the GUI where I specify to only check stored procedures (I've simplified the filter down for this example). Here's the batch file (simplified):

We will contact you directly about this, as the problem sounds like it needs some serious debugging.

If you want to avoid error code 63, you're supposed to use the /include:Identical switch, but then you include all objects, which may or may not override your filters (the results of using command-line options with conflicting project options are inconsistent).

Either way /reportAllObjectsWithDifferences shouldn't suddenly be reporting all objects as different when they're not.